The flood are not destroyed in any way, there are still flood spores one some halo rings and somewhere in the universe still flood controlled planets. There is a spartan-iv training program to train against the flood. Infection in the halo 4 MP is one of those. However they are just an assumption to what they could become.
The most horrifying thought is a flood infected spartan. A trained killing machine, with an armor capable of lifting tanks. The flood themselves ar known to overstep the physical boundaries their host is capable off, it would be a complete nightmare if one ever existed.